Fig. 3. Single tubule ATAC-seq for microdissected proximal tubules from Sham and UNx at the 24 h timepoint.

a Ratio-intensity plot. Points represent peak regions determined by MACS2 for individual peaks. The x-axis represents average signal intensity within the region, and the y-axis represents log₂ ratio of Sham and UNx signals. Red line is Loess fit. Among the 125,973 open chromatin regions identified among all samples, 4223 were identified as differentially accessible sites (FDR < 0.05, highlighted in magenta). (n = 3 for each group) b HOMER analysis identifies the enriched TF binding motifs in chromatin regions that are more accessible in UNx vs Sham (applying cumulative hypergeometric distribution adjusted for multiple testing with the Benjamini-Hochberg method) (See also Supplementary Data 5 for all results). c Percentages of motif sequences in all peaks (white) or in differentially accessible regions (grey) for the PPARα/HNF4α target motif and the HNF1B target motif. d Transcription factor foot-printing profiles generated using all identified ATAC-seq peaks for PPARα and CTCF (negative control) for microdissected PT-S1 to quantitate Tn5 insertion enrichment in the UNx vs. sham. e Volcano plot indicating peaks of chromatin accessibility within annotated promoter-TSS regions. Magenta points, increased accessibility in the UNx vs Sham treatment (FDR < 0.05 and log₂(UNx/Sham)> 0.5). Blue points, decreased accessibility (FDR < 0.05 and log₂(UNx/Sham) < −0.5). Chromatin accessible regions with top 10 or bottom 10 log₂(UNx/Sham) values annotated by nearest gene name. f Volcano plot indicating chromatin accessibility at promoter regions near annotated TSS. Magenta points, PPARα target regions. Target genes for PPARα are listed in Supplementary Data 7. g Examples of ATAC-seq peaks for known PPARα and HNF4α target genes, each showing differences in peak heights between UNx and Sham treatments at their promoter-TSS regions (highlighted in green; DAR, differentially accessible region, vertical axes are of equal length). All data are available on a genome browser at https://esbl.nhlbi.nih.gov/IGV_mo/ and a Shiny-based web page (https://esbl.nhlbi.nih.gov/UNx/). * FDR < 0.05 (Benjamini and Hochberg method, adjusted p values are provided in Supplementary Data 6).